Halo Chronicles: Return of the Flood
by pkmnMasterChief2010
Summary: I WON'T BE UPDATING THIS STORY ANYTIME SOON. Cortana has to make a big decision in her life on Earth after her valiant efforts in the war/Thel Vadam seeks help from the UNSC to fight off a Flood infection on the Sangheili homeworld, Sanghelios.
1. Rescue and Reunion

**DISCLAIMER: I DON'T OWN THE RIGHTS TO HALO OR ANY OF ITS CONTENT. THE STUFF I JUST MENTIONED IS THE PROUD PROPERTY OF MICROFOFT GAME STUDIOS AND 343 STUDIOS.**

_**The Story up to This Point...**_

_John-117 (aka The Master Chief) and Cortana have been living on the stern-half of the Dawn for the last 1 month. Cortana has sent out a distress call to anyone willing to help out. After that, Cortana had been watching Chief sleep in cryo for a few years. That's the just of it. Now, Cortana is attempting to wake up the Master Chief for a very good reason..._

"Chief, Chief!" cried a voice. "Chief, wake up!"

"Ugh, Cor... Cortana?" he replied weakly. "What's going on?" Cortana pointed to the blackness outside the remains of the Dawn. "Is that a slip space rupture?"

"We're being contacted," Cortana reported. It's from..."

"From what?" Chief slowly emerged from the cryo chamber he was encased in.

"Listen for yourself," she replied. Cortana began to fine tune the radio for a clear signal. All they heard for a while was some static. Finally, the static went away.

"... I repeat, this is Thel Vadam aboard the Shadow of Intent. Chief, Cortana, if either of you acknowledge, respond," the voice continued.

"Finally," Cortana began, "we can get out of here. John, we can go home!"

"Yes... home." Chief activated some controls and began speaking again. "Thel Vadam, this is SPARTAN-117. We read you loud and clear. If you could send us a Phantom, we could get out of this goddamn thing."

A few minutes passed. Chief and Cortana were being escorted by the 'Rtas Vadum, the Ship master of the Intent, to their quarters. "I hope you find your accommodations satisfactory," Vadum told them then left.

"What should we do now, Chief?" Cortana asked as she appeared on the holo-emiter. "Chief?" There was just silence. "Chief, could I see your face?" He continued to look out the window, remaining silent. "Is there something wrong?" He responded with a nod. "You want to talk about it?" He turned to Cortana. He moved closer, as if he was expecting something to happen.

"Cortana, what will happen to us when we get back to Earth?" the armour clad Spartan began. "All my life, I've been fighting in a war." He paused. "And most of the time, it been with you by my side..."

"You don't need to say anything else, John. I think i get it." She got as close to him as she could. "You're afraid you'll never see me again." He stayed silent and just sat in the stool. "Chief, you're in love with me, aren't you?" Chief didn't respond. "To tell you the truth, I've always had a thing for you, John." If it was an attempt to get his attention, it worked. "Chief, I... I... I can't be away from you." It seemed as if Cortana was about to burst into tears. "I love you, John. When I'm not with you, I feel so lost, so alone, but when I am with you, I feel safe, secure, loved..."

"Cortana," Chief interrupted, "I get the picture. Truth is, I've always had a crush on you. Always have. When you captured by Gravemind, memories of you get coursing through my mind; I couldn't get you out of my head." They remained silent for a few minutes. Chief reached for the holo-emiter; Cortana intercepted his hand and held it to the best of her ability. "Only one problem..."

"What i... oh. Right. But, still..." Cortana stopped in her tracks. She knew that trying to win an argument against the Chief was not a good idea. "...there might be a way to change me into a human but..."

"...but, there isn't. And besides, do you think you would be able to mingle with the rest of society without confusing them to death or revealing that you are an AI?"

"I know, but, if there is... would you still be by my side?" This time, the Chief said nothing. Cortana remembered this action. It was one of his ways of saying that the conversation was over.

"I'm going to the bridge." He walked out of the room, leaving Cortana behind.

On the bridge, the Sangheili crewmen were having a somewhat formal party. Everyone was having a good time.

The helmsman raised from him chair, raised his glass and declared, "A toast, to the man who might have just saved the home world, Thel Vadam."

"Here, here," was the response given by everyone on the bridge.

"And, a toast, to an old friend," a voice emanated from the direction. It was the Chief, with a glass raised.

"I'll drink to that," Thel said raising his glass. After the party, the Arbiter escorted the Chief back to his quarters.

"Okay," said the Chief.

"What?" Thel asked.

"What's the real reason you came to find me?"

"My science staff found a massive natural energy source in the mountains, and shortly after, a Flood infected UNSC ship landed in the area. We managed to contain it within a massive force field, but, I'm not sure how long it will hold them."

"And you want me to be the exterminator?"

"Something like that."

"I'll think about it... as soon as we get back to Earth."

Thel nodded and said, "Thank you." The door to the Chief's quarters slid open and he began to enter. "And John..." The Chief stopped in mid stride; he looked at the Shangheili Arbiter. "It's good to have you back, my friend." He nodded and the door closed behind him.

Chief walked in to see Cortana _'sleeping'_. She _'woke up'_ a little while after Chief sat down. "What was that about?" When she looked at him, she couldn't believe what she was seeing; the Chief had his helmet off. "Chief... what's wrong?"

"There's a situation on Sanghelios," the Chief started. "A Halcyon-class cruiser matching the description of the Pillar of Autumn landed in the mountains." He gazed at Cortana. He saw fear in her eyes. "Cortana, I'll figure out what to do when we get to Earth."


	2. Return Home to Surprise

With the Shadow of Intent in Earth's orbit, Thel Vadam, 'Rtas Vadum, John-117, and Cortana were met by Lord Terrence Hood at the Traxus Shipyard in New Washington. With a military escort, Lord Hood took them to ONI ONYX Base, where they were debriefed on everything that went down.

"...so then we found the Chief, I briefed him on what's happenning on Sangehelios, and brought him here." Thel Vadam had finished what he had to say.

"Well," Lord Hood began, "I guess that covers everything we need to talk about." He looked at the Master Chief. "Something bothering you, Chief?" The Chief was staring at the floor. He seemed to pondering something. "Chief!"

"Oh, yes, sir." The Chief snapped out of it.

"Something wrong?"

"Actually, yes. When me and Cortana were drifting in space, we came across what seemed to be a Forerunner space station. The only question I have about it is that why was it so far out there?"

"I'm sure we'll figure it all out. Dismissed." Thel, 'Rtas, and Chief all began to walk out of the room. "Chief..." The Chief looked at Hood. "Dr. Halsey wanted to see you in her lab. Said it was urgent, but, she didn't say what it was."

"I'll stop by on my way out... sir." He continued to walk out.

Terrence Hood sat back down at his desk. _'He hasn't changed one bit. I wonder why that structure was out so far. No matter... it's good to have the Chief and Cortana back home.'_

* * *

><p>Dr. Halsey was in her office, surounded by books, computers, papers, all her research. She was reading a book. The door slid open. "Dr. Halsey, someone here to see you, a Spartan to be exact," one of the researchers said.<p>

"John-117," she responded. "Send him in." The reasearcher nodded and motioned for Chief to enter. "John, have a seat, please." He did as she said. "Do you have her?" He nodded. "Say the words, please."

"I have her, ma'am," responded the Chief.

"Good." Halsey raised from her chair. "Give mer her chip." Again, he obeyed her. The chief pulled the chip out from the back of his helmet and put Dr. Halsey's hand. She inserted the chip into her conputer, just as she did, Cortana appeared in a lifesize hologram. "Cortana, how are you systems opperating?"

"Considering I'm nearing the end of my lifespan, I'm doing surprisingly good. No malfunctions to report, at least, not now," was the somewhat lengthy response from Cortana.

"That's good. Now, if you two would come with me, I have something to show each of you." They began walking to a storage area. "Chief, you probebly don't know this, but since you and Cortana went missing, I began developing a new model of the MJOLNIR Powered armour." The door opened to reveal a suit of armour. "Chief, I reveal to you the MJOLNIR Mk. VII Powered Armour suit. Fully equiped with built-in drop shield, armour lockup, active camouflage, zero gravity thrusters, and jetpack. Finally, since the UNSC has an alliance with the Sangheili government, we have managed to get our hands on an enhanced shielding system."

"Well, Dr. Halsey..." the Chief began.

"John, your one of the first Spartans I ever trained, and, well, we've known eachother for a long time. So, please, call me Cathrine."

"Cathrine, I have to admit, you continue to amaze me. You even took the liberty of changing the armour design. However..." He paused for a minute. "How good are the shields against the Flood?"

"I beg your pardon?"

"Thel was telling me about a situation on Sanghelios. Aparantly, a ship matchng the discription of the Autumn has landed in the mountains, there. So, how good are the shields against the Flood?"

"First of all, we didn't expect for the Flood to return, so we haven't tested it on actual subjects, and second, the Pillar of Autumn was destroyed in the Battle of Installation 04."

"That's what I thought, but, what if the Flood somehow manage to get it opperational again?"

"Chief," Cortana started, "It couldn't be the Autumn. I remember seeing it be blown to peices..."

"Then how do you explain the Autumn's insignia on the bow?" Cortana looked puzzled, as did Halsey.

"Why don't we drop this conversation for another time," Halsey began. "Cortana, I've got something to show you, too. Come with me."

They walked down the long hallway to an elevator. Halsey pressed the buttom to go down, the door slid shut and the elevator began to decend. When the doors openned again, the Chief and Cortana couldn't believe what they were seeing. "This is my personnal laboratory. It houses my _personal_ projects, like the one I'm working on now."

"What are you doing down here, Doctor?" Cortana inquired.

"Come with me, and I'll personally show you both," Halsey responded. A quick walk down the viewing platform and down a staircase on the left lead to a opperating table with a body, wearing a hospital gown and undergarmets, on top of it. The table was sorounded by machines like none niether Cortana or Chief ever seen before. "What I am doing is testing if an Artaficial Inteligence program can be moved into a human brain. Theoretically, it should work, but, in order for it to work, we need a non-living body for the operation, like a clone that's not breathing, so, again, theoretically, we could turn an AI into a living, breathing, human being." Cortana's eye's began to glow with exitement. "Only one problem; we haven't been able to test it. Cortana, would you like for you to be the one to test it for me. You don't have to decide right now; seriously, take all the time you need."

"I... I... I don't know," Cortana started. "I know my life-cycle as an AI will be over in about one year. Would I age normally luke everyone else?" Dr. Halsey nodded. "And keep all my memory?" Again, Halsey nodded. Cortana pondered this idea for a few minutes. "Chief, what do you think?"

"I honestly think that this procedure is dangerous," began the Chief. "For instance, how is Cortana supposed to get inside the brain?"

"I'm sure Dr. Halsey has the entire thing figured out, like I've figured out this will likely be a one-way trip."

"You're right, Cortana," Halsey responded. "It is a one-way trip and I do have how you're going to get into the brain figured out. You think about it, and, Chief, feel free to take the Mk. VII armour on your way out. You to should both go and get some rest."

"Of course, ma'am," the Chief responded.


	3. A New Beginning

On the way out, Chief took Cortana's chip out of Dr. Halsey's computer and inserted it into his new Mk. VII helmet. Upon exting the elevator, he was called over by a marine.

"What is it, marine?" asked the Chief.

"Lord Hood sent me to tell you we wanted to talk to you," replied the marine. Chief nodded and continued on his way. He entered Lord Hood's office to see Hood standing at the door.

"Chief," Lord Hood began, "you've been fighting for a long time, and I can't remember the last time you got a vacation. So, I'm give you a one year leave."

"Sir..." Chief started.

"This is not up for debate, Chief. Just enjoy it."

"Yes, sir."

Chief exitted Hood's office, remembering what Lord Hood told him. He walked down to his quarters, entered, placed Cortana's chip in the Holo-emiter, and went to sleep in his bed. 

The next morning, Chief awoke to Cortana hovering above him. "Morning, Chief," she started. "How'd you sleep?"

"How are you even... you know what, nevermind. I slept well."

"Chief, I was thinking last night... maybe I should take Dr. Halsey up on her offer. I want to know what it's like to be human..."

"Okay, go for it. If you think I'm going to stop you, I'm not. Actually, I'm all for it."

"Really?" In response, the Chief nodded. "Thanks, Chief. Will you come for the opperation?"

"Of course."

The reaction that she recieved from Chief surprised her, but, she embraced it, kissing him on the side of his helmet. "Alright, then. I'll talk to Dr. Halsey about it as soon as possible."

Down in the lab, Dr. Halsey was in the middle of reading one of her books on transfering data from a hard drive to another when the Chief walked in on her.

"Who the hell said you could come in here!" she yelled without taking her eyes off her book.

"Cortana wanted to speak to you, ma'am," the Chief responded calmly.

"Oh... sorry, John; I thought you were one of the staff members."

Chief handed Cortana's chip to Halsey and she inserted it into her computer. Again, Cortana appeared in a life size form.

"Dr. Halsey, I've actually decided I want to do the first test. I want to become human," Cortana declared.

"Alright," Halsey began, "if you want we could do this right now. Chief, would you mind assisting me?"

"Of course," he replied. "Cortana is my closest friend after all." Cortana began to, literally, turn pink.

They went down to Halsey's personal lab, where they were about to start the procedure. "Everything shows green. Cortana, when your ready..." Dr. Halsey didn't need to say anything else, because the transfer had already begun. "Transfer complete. Chief, turn on the medical equipment, and ready the difibulator." Chief nodded and plugged it in. As Chief did that, Dr. Halsey pulled the transfer cable out of the body's left ear. "Alright. Clear!" Just as the body jumped, the electrocardiogram picked up a pulse. "Yes! Chief, we did it; we successfully transfered an AI to a human brain!"

"Ya. We did... wait, who's body did you clone?"

"No ones. What I did was genetically change my son's DNA so that it would be a female, and I cloned that into a human being."

"Ah."

A few minutes later, Cortana, in her new body, woke up to see the Chief and Dr Halsey looking at her. "Chief, did... did it work?" He nodded.

"Cortana," Dr. Halsey started, "I need to run some tests. They are real simple. First, try moving you fingers." Cortana did so. "Good, now your arms." She moved them, amazed that she was actually doining it. "Toes." She moved them. "Legs." She abliged with success. "Now, try to sit up." Cortana managed to sit up with a little difficulty. "Now, try to stand up." Again, she did so with a little difficulty. "Now, try walking towards John." She tried, almost with every step stumbling. She almost reached him when she tripped over herself; luckilly, Chief caught her. "Good. Well, everything checks out." Halsey walked over to the new Cortana. "Cortana, I'm so happy for you right now. I just hope you enjoy your new life. I also talked to Lord Hood; he told me, since your a civillian now, you should be paid for your years in service to the UNSC. He's set you up with a home and everything."

"Well," Cortana began, "I guess I should go thank him properly then."

"I will escort you, since your not used to walking on solid ground yet," Chief said with a grin under his helmet.

"Wait." Halsey stopped them. "If your going to go into society, you need some clothing... I should have some in the back. I'll get them." Five minutes later, Dr. Halsey returned with a blue dress, blue jeans, and a purple t-shirt. "Here, try these on."

"Okay." Cortana took off the hospital gown tried to put the t-shirt on first. She got it on with the third try. Next, she tried to put on the jeans, which she got right away. She took those off and tried on the dress; she realized it was almost the same as putting on the t-shirt. "So, how do I look?" Halsey kept her mouth shut realizing the question was directed at the Chief.

"You look beautiful, Cortana," he finally said after about two minutes of staring at her. "Should we go?"

"Yes," Cortana began, "We should. Bye, Dr. Halsey; thanks for everything."

After fending off about fifty marines, Cortana and the Chief arrived at Lord Hood's office. Cortana had gotten used to walking. The door openned. "Cortana, as Dr. Halsey might have told you, I've taken the liberty of starting you out for your life. I also want to give you this."

"It's... a... pass to get into any of the UNSC or ONI bases across the world." Cortana was a little confused. "Why would I need this?"

"Because, now, Cortana, you're a civilian. And, well, we just can't let everyone into one of the bases. With this, you can enter them without being shot. And, also, if you do decide to visit, you won't be aloud to access every area. Clear?" Cortana nodded. "Good. Remember, you're always welcome to visit me or Dr. Halsey anytime. As for you, Chief, I gave you a leave. Why the hell haven't you left base?

"I have nowhere to go, sir," Chief responded.

"Chief, you could come to my house if you want," Cortana suggested.

"Alright then, I've got nothing better to do." Chief and coortana began to leave the room.

"Cortana." She stopped and looked at him. "You'll need these, too. The keys are for your car that I have waiting for you outside, and the map has where you live indicated on there."

"Thank you, sir." They exitted the room with the door shut behind them.

_'I hope she doesn't get herself lost. Not to worry, Chief's with her; they'll be fine." _Terrence looked at the picture of his family that he lost when New Mombasa was destroyed.

"Hey, Cortana."

"Yes, Chief?"

"I was just looking through the Ml. VII armour's abilities and it can detach from my body and fold into a suitcase."

"That's... actually rather impressive, Chief. Now, no one nut me will know who you really are when we get to our new neighborhood."

"Perfect for keeping a low profile." The conversation lasted until Chief and Cortana pulled into the driveway of Cortana's new home.


End file.
